Navmesh agent doesn't detect baked navmesh.

We are using the new Unity navigation. And it has always worked fine until something broke the game.

Each time we bake the scene , we can see the navmesh appear in the level. But when we run the game the navmesh dissapears. The AI's aren't able to find a surface. When we stop the game the navmesh is also removed from the scene. But the navmesh is added to our project folder. We have no clue what the problem is.